MolNFT v1 · #190599 · protein
Cryo-EM structure of pseudomonas aeruginosa rnap sigmas holoenzyme complexes with transcription factor suta (open lobe)
7XL3 · DNA-directed RNA polymerase subunit alpha: “Cryo-EM structure of pseudomonas aeruginosa rnap sigmas holoenzyme complexes with transcription factor suta…”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.81).…
- PDB
- 7XL3
- Type
- protein
- Length
- 3,480 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase subunit beta…
- EC
- 2.7.7.6
- UniProt
- O52760, Q51561, Q9HWC9, Q9HTM1, Q9HTR9, P45684
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 7 distinct chains · 31% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 217 | 17% helix, 36% strand | O52760 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 216 | 18% helix, 32% strand | O52760 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1324 | 28% helix, 21% strand | Q51561 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1338 | 33% helix, 15% strand | Q9HWC9 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 71 | 61% helix, 0% strand | Q9HTM1 |
| G | Transcriptional factor suta | protein | 37 | 43% helix, 5% strand | Q9HTR9 |
| F | RNA polymerase sigma factor rpos | protein | 277 | 52% helix, 2% strand | P45684 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 784 | 0.81 | 0.85 | 76 | empty |
| 2 | 520 | 0.81 | 0.87 | 65 | empty |
| 3 | 913 | 0.80 | 0.82 | 110 | empty |
| 4 | 874 | 0.79 | 0.82 | 82 | empty |
| 5 | 1186 | 0.78 | 0.80 | 107 | empty |
Interfaces
11 interfaces between chains.
- C–D · 8251 Ų buried · 83 hydrogen bonds · protein-protein
- D–F · 2349 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1834 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1550 Ų buried · 14 hydrogen bonds · protein-protein
- C–F · 1395 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7XL3 · Cryo-EM structure of Pseudomonas aeruginosa RNAP sigmaS holoenzyme complexes with… · the same entry in another collection · chain F against F, TM-score 1.00
- Q51561 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (Q51561) · a predicted model of the same protein · chain C against A, TM-score 0.97
- Q9HWC9 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (Q9HWC9) · a predicted model of the same protein · chain D against A, TM-score 0.92
- O52760 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (O52760) · a predicted model of the same protein · chain A against A, TM-score 0.90
- Q9HTM1 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (Q9HTM1) · a predicted model of the same protein · chain E against A, TM-score 0.88
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O52760
- Every structure of UniProt Q51561
- Every structure of UniProt Q9HWC9
- Every structure of UniProt Q9HTM1
- Every structure of UniProt Q9HTR9
- Every structure of UniProt P45684
- Elsewhere: RCSB PDB 7XL3 · PDBe 7XL3 · UniProt O52760 · UniProt Q51561 · UniProt Q9HWC9 · UniProt Q9HTM1 · UniProt Q9HTR9 · UniProt P45684
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.